[gmx-users] local pressure calcuation for Gromacs-4.5

Wed Jun 15 23:08:24 CEST 2011

Dear all,

Could anyone direct me to the manual for local pressure calculation or a
place where everything is mentioned about it ? I have been only able to
collect bits and pieces from the mailing lists.

Thank you
Amit

On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 15/06/2011 9:09 PM, Jianguo Li wrote:
>
>  Dear all,
>
> I have made a test calculation of local pressure using version 4.5 for my
> membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives
> the localpressure data. Howeve, instead of giving an anveraged data of the
> local pressure, mdrun gives a separate file for each frame, so I got many
> files: localpressure.dat0, localpressure.dat1, localpressure.dat2,
> localpressure.dat3 ......
> Then I need to calculate the pressure tensor for each frame and make
> average. but these localpressure.dat files are very big (each file is about
> 30 Mb), occupying large space of the hard disk. Can anyone give some
> suggestions on how to fix this? Thank you very much!
>
>
> I would expect that the output frequency is configurable, but can only
> suggest you consult what documentation exists for this version. Your main
> alternatives are
>
> * to compress the files with (say) bzip2 or (less effective) gzip and
> construct a script to uncompress them singly and analyse them "on the fly"
> (AMBER users do a bit of this kind of thing, Google around)
> * to discard ones that are too frequent. However, judging from the numbers
> below, every 100ps is probably OK.
>
> Mark
>
>
>  The command is:
> mdrun_d -s lp.tpr -rerun box_md5.trr -x box_md5_rerun.xtc -o
> box_md5_rerun.trr  -g md5_rerun.log -localpgrid 0.1
> And the output message is:
> ........
> Dumping local pressure based on 1 frames to localpressure.dat0...
> Reading frame       2 time 119400.000
>
> Dumping local pressure based on 1 frames to localpressure.dat1...
> Reading frame       3 time 119500.000
>
> Dumping local pressure based on 1 frames to localpressure.dat2...
> Reading frame       4 time 119600.000
>
> Dumping local pressure based on 1 frames to localpressure.dat3...
> Reading frame       5 time 119700.000
>
> Dumping local pressure based on 1 frames to localpressure.dat4...
> Reading frame       6 time 119800.000
> .......
>
> Cheers,
> Jianguo
>
>
>
>  ------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu> <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org><gmx-users at gromacs.org>
> *Sent:* Friday, 10 June 2011 07:10:35
> *Subject:* Re: [gmx-users] local pressure calcuation for Gromacs-4.5
>
>
>
> Amit Choubey wrote:
> > Thanks Justin, I tried to install the recent git version but the
> configure file is missing. How should I install this version ?
> >
>
> Run the bootstrap script.  It generates the configure script.
>
> -Justin
>
> >
> > On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
> jalemkul at vt.edu>> wrote:
> >
> >
> >
> >    Amit Choubey wrote:
> >
> >        Dear all,
> >
> >        I saw an unanswered post at
> >
> http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html
> >
> >        It is about calculating local pressure in v 4.5 when using
> >        CHARMM FF. Could someone give me some pointers about this?
> >
> >
> >    I don't know what the development status of version 4.5 is, but you
> >    can access it at:
> >
> >
> http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
> >
> >    It hasn't been merged with release-4-5-patches in some time, so many
> >    resolved bugs won't be fixed.
> >
> >    -Justin
> >
> >    --    ========================================
> >
> >    Justin A. Lemkul
> >    Ph.D. Candidate
> >    ICTAS Doctoral Scholar
> >    MILES-IGERT Trainee
> >    Department of Biochemistry
> >    Virginia Tech
> >    Blacksburg, VA
> >    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> >    <tel:%28540%29%20231-9080>
> >    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> >    ========================================
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>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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